[mira_talk] Re: change stringency in Mira mapping assembly

From: Bastien Chevreux <bach@xxxxxxxxxxxx>

To: mira_talk@xxxxxxxxxxxxx

Date: Tue, 17 Jan 2012 00:15:29 +0100

On Jan 16, 2012, at 23:33 , Christoph Hahn wrote:
>> Via a detour: make a simple list of the reads you want to keep and use
>> "convert_project -n"
> Tried that. Created a file called list.txt containing a list of reads like
> this:
> @PCUS-319-EAS487_0005_FC:8:1:3863:1082#0/1
> [...]
> then ran convert_project -f maf -t fastq -n list.txt readpool.maf test
> again, the test.fastq file stays empty. See stdout below. What do I do wrong?
The @ sign in FASTQ files is not part of the sequence identifier (aka: sequence
name). See also: http://en.wikipedia.org/wiki/FASTQ_format
convert_project expects you to give names, therefore leave out the @ sign in
that list:
PCUS-319-EAS487_0005_FC:8:1:3863:1082#0/1
...
B.
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